AIMC Topic: Protein Binding

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Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes.

BMC bioinformatics Dec 9, 2015
BACKGROUND: Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been develo...
Area Under Curve Support Vector Machine Hydrogen Bonding Proteins Protein Structure, Tertiary Principal Component Analysis ROC Curve Dimerization Protein Interaction Maps Protein Binding
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Identification of Peptide Inhibitors of Enveloped Viruses Using Support Vector Machine.

PloS one Dec 4, 2015
The peptides derived from envelope proteins have been shown to inhibit the protein-protein interactions in the virus membrane fusion process and thus have a great potential to be developed into effective antiviral therapies. There are three types of ...
Viral Envelope Proteins Support Vector Machine Sequence Analysis, Protein Peptide Fragments Viral Fusion Protein Inhibitors Protein Binding
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A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Dec 3, 2015
BACKGROUND: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands...
Algorithms Molecular Docking Simulation Protein Binding Proteins Machine Learning Data Interpretation, Statistical Pattern Recognition, Automated Protein Interaction Mapping Models, Chemical Binding Sites Sequence Analysis, Protein Ligands
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Prediction of Protein-Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures.

The Journal of membrane biology Nov 12, 2015
Accurately predicting protein-protein interaction sites (PPIs) is currently a hot topic because it has been demonstrated to be very useful for understanding disease mechanisms and designing drugs. Machine-learning-based computational approaches have ...
Binding Sites Protein Interaction Mapping Protein Binding Machine Learning Databases, Protein Reproducibility of Results Computational Biology Workflow Models, Molecular Proteins Protein Conformation
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Prediction the Substrate Specificities of Membrane Transport Proteins Based on Support Vector Machine and Hybrid Features.

IEEE/ACM transactions on computational biology and bioinformatics Nov 11, 2015
Membrane transport proteins and their substrate specificities play crucial roles in a variety of cellular functions. Identifying the substrate specificities of membrane transport proteins is closely related to the protein-target interaction predictio...
Support Vector Machine Models, Chemical Pattern Recognition, Automated Membrane Transport Proteins Algorithms Molecular Docking Simulation Protein Binding Sequence Analysis, Protein Binding Sites Substrate Specificity Protein Interaction Mapping
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Gapped sequence alignment using artificial neural networks: application to the MHC class I system.

Bioinformatics (Oxford, England) Oct 29, 2015
MOTIVATION: Many biological processes are guided by receptor interactions with linear ligands of variable length. One such receptor is the MHC class I molecule. The length preferences vary depending on the MHC allele, but are generally limited to pep...
Epitopes Histocompatibility Antigens Class I Sequence Alignment Protein Binding Computational Biology Peptide Fragments Neural Networks, Computer Algorithms Humans
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Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

Immunogenetics Sep 29, 2015
A key event in the generation of a cellular response against malicious organisms through the endocytic pathway is binding of peptidic antigens by major histocompatibility complex class II (MHC class II) molecules. The bound peptide is then presented ...
Epitopes Amino Acid Sequence Binding Sites Histocompatibility Antigens Class II Cluster Analysis Molecular Sequence Data Algorithms Databases, Protein Sequence Homology, Amino Acid Humans Animals Protein Binding Models, Molecular Neural Networks, Computer Mice Peptide Fragments Computational Biology
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Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME.

Database : the journal of biological databases and curation Sep 16, 2015
Today's large, public databases of protein-small molecule interaction data are creating important new opportunities for data mining and integration. At the same time, new graphical user interface-based workflow tools offer facile alternatives to cust...
Humans Drug Interactions Protein Binding Animals Pharmacokinetics Drug Discovery Proteins Knowledge Bases Pharmaceutical Preparations
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Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands.

Journal of chemical information and modeling Sep 4, 2015
The magnitude of the investment required to bring a drug to the market hinders medical progress, requiring hundreds of millions of dollars and years of research and development. Any innovation that improves the efficiency of the drug-discovery proces...
Models, Biological Ligands Molecular Conformation Receptors, Estrogen Drug Discovery Protein Binding Estradiol Neural Networks, Computer Databases, Factual Computer Simulation Humans
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idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking.

Journal of computational biology : a journal of computational molecular cell biology Jul 29, 2015
Predicting the three-dimensional native structures of protein dimers, a problem known as protein-protein docking, is key to understanding molecular interactions. Docking is a computationally challenging problem due to the diversity of interactions an...
Protein Conformation Binding Sites Protein Multimerization Computational Biology Proteins Ligands Algorithms Molecular Docking Simulation Protein Binding Machine Learning
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